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I always get errors and mistakes concerning overuse or underuse of commas.
Personally, outside some obvious situations I feel the use of commas is purely optional and dependent on whether you want to use it or not
E.g "I liked the inclusion of a green bear in the story, which really helped the plot"
In this situation, I don't have to use a comma, but if I didn't, i could be penalised by one reviewer for doing so, and if i didn't, I could be penalised for omitting it
It's all just confusing

I totally agree, and I'm facing the same problem. I can't find a clear guide on it either. One editor will see that you miss commas, when I use them, the other editor sees excessive use of it. Not sure how to get that right.

Comma discrepancy can vary widely; this is because there is much debate regarding proper comma usage, particularly in the realm of individual writing styles. Stylistic preferences of the reviewer/writer should be taken into consideration and not count against them unless there is a justifiable reason for doing so. This does not mean that there aren't plenty of areas where using or not using a comma is simply incorrect.

In the first sentence you've listed, I would argue that the comma is necessary because removing it makes the sentence hard to read (creating a run-on). There are other technical terms that justify its use in that context, but ultimately, it just makes the sentence clunky. However, if you change "which" to "that," you can then argue the use or omission of a comma, because the properties for "that" and "which" are not the same. There are semantics and subtleties involved in the English language that can be confusing to keep track of, even for people who have been reading and writing for most of their lives.

If you believe that you were unfairly counted against including/omitting a comma, I would highly recommend that you ask for a recheck/admin recheck. I have had multiple scorecards readjusted because the reasoning that the editor gave was weak/opinionated vs academically substantiated. As long as you can justify its initial use--and can provide reasoning/evidence from academic sources--you have grounds to defend your work. Don't be discouraged. (:

In the standard English language, you always have to use a comma before which. There is never a comma before the word that. If you use any of the coordinating conjunctions-for, and, nor, but, or, yet, so-to join an independent clause with another independent clause, then you must put a comma before it. You must use a comma after an introductory phrase or clause. You also use two commas to separate a non-essential element from the rest of a sentence. By the way, a non-essential element is a word or a set of words that the sentence can do without. Non-essential elements are used to provide clarity.

Here are a few examples to get my point across.
1. My country, Nigeria, will become better.
Explanation- In this sentence, Nigeria is a non-essential element so I used two commas to separate it from the rest of the sentence.

2. I like rice, but I hate beans.
Explanation- In this sentence, but is functioning as a coordinating conjunction because it's connecting two independent clauses.

3. I like rice. However, I hate beans.
Explanation- Words like however, furthermore, moreover, etc are conjunctive adverbs. You must put a comma after them. They cannot be used to join two independent clauses.

This is the brief explanation, but it really helped me. I bet you to try it as well.

Thank you for clarifying this very confusing matter. I have had a big problem with commas when writing my reviews.

Thank you for this clarification. I have found the same problem, with one reviewer saying no comma is needed and another scorecard saying a comma is needed. I am wondering if it is a British vs. American issue?  Here is an example from one of my reviews:

Editor Comments:
But Julie has a secret, one that could destroy her family, and one that she must guard at all costs if she is to be considered good enough to marry the gorgeous and successful Calvin Sexton.[remove the unnecessary comma after "family"]

Sorry, I meant to add; perhaps someone can help me out? Is the comma necessary, acceptable, or not? The other scorecard did not mention it. 

Using commas and "and":

It seems the use of commas is getting the better of me, and I'm being overtaken, aaarrrghhh!! Lol.

Just want to say "Big Thanks" to the review editors. I learnt a new thing this week, about the use of the comma and the conjunction "and". I never knew a comma was needed in pretty much all uses of the word and, even in a list. I always thought the last "and" when listing many items didn't need that last comma just before. Going through the forums, I've just learnt about the "Oxford comma", and that it is grammatically optional to use or to not use the final comma in a list before the "and".

I've googled it a bit now though, and although the internet doesn't have everything, I've found enough to teach me otherwise about commas and "and". Thank you to the review editors for highlighting that, and allowing me to learn and grow.